About the Project
Natural Environment Research Council funded RED ALERT Centre for Doctoral Training will provide training in water-based early warning systems for environmental and public health protection focused around 4 UK and 3 international Living Labs aimed to provide the in-depth knowledge and enable a step-change in managing environmental and public health.
Molecular techniques are moving towards detecting pathogens and freshwater organisms in real-time. This is hindered by challenges in the characterisation of trace-level environmental DNA (eDNA) and complex bioinformatic analyses of metagenomes. Targeted approaches, e.g. qPCR and metabarcoding can rapidly assess pathogens and wildlife, but miss non-target organisms and emerging threats. Metagenomics captures everything, but is biased towards smaller and more numerous genomes (microbes/viruses), while wildlife eDNA is only present in trace amounts which hampers detection. Beyond these physical limitations, analysis of sequence datasets from both Illumina (short reads, longer turnaround) and Oxford Nanopore sequencing (longer reads, on-site turnaround) needs to be optimised to speed up identification of pathogens and wildlife.
Aim
Investigate how selective sorting of organisms and DNA from the environment, combined with improved sequence processing can speed-up identification of pathogens and freshwater organisms to assess river health. Combining size fractionation, optimised DNA extraction and combinatory bioinformatic approaches (short and long-read sequencing), we will streamline detection of viral/prokaryotic/eukaryotic diversity and address the pollution challenges in the Conwy catchment, North Wales, one of the focal ecosystems for the RED-ALERT CDT.
Objectives
Optimise bioinformatics tools using existing Illumina metagenomes. Long-read Nanopore sequencing will improve identification with real-time outputs.
Characterise the river water using size-fractionation (<0.22-80μm; Power et al 2023), combined with differential eDNA extraction techniques (organismal/extracellular/viral), to improve detection efficiency and quantification using targeted and metagenomic approaches.
Co-design pathogen surveillance, human and wildlife exposure risks with Partners Afonydd Cymru, Natural Resources Wales and CASE partners North Wales Rivers Trust.
Case studies
Test optimised tools on real-life scenarios, e.g. detection of wildlife pathogens; assess impact of river health on salmon disease.
Outputs: RED-ALERT tools
A pathogen traffic light system will be designed to flag significant levels of viral, bacterial and eukaryotic pathogens and community composition using a real-time molecular toolkit.
The student stipend is £19,237 per annum, with all fees and other costs covered.
Experience and interest in some of the following areas would be desirable, but we would not expect a candidate to possess all skillsets featured below and training will be provided throughout the PhD.
· Field work. Water samples will be collected from the Conwy river and catchment.
· Molecular biology. The project will involve DNA extraction and concentration, PCR, qPCR, sample preparation, quality control and sequencing using Illumina and Oxford Nanopore platforms. Knowledge, understanding and experience of environmental DNA will be used to assess freshwater communities and river health.
· Bioinformatics. A large part of the PhD will be require the analysis and interpretation of sequence data and molecular biology techniques. Several bioinformatics tools are available and need to be tested to build a robust and efficient pipeline to rapidly analyze sequence data and flag organisms and community composition that indicate poor river health.
· Pollution and microbiology. The project will identify and characterize pollution events from agriculture, wastewater, hospitals, septic tanks and other human activities that can impact freshwater ecosystems. Pollution sources will be determined using chemical analysis combined with identification of indicator species from sequencing. Assessment of pathogen load and composition will be needed to build a wide picture of pollution and community health. This will be achieved through sequence analysis of viruses, bacteria, protozoa and eukaryotic pathogens and parasites.
· Freshwater biology and ecology. To interpret the eDNA analysis it is vital to understand the river community and composition in terms of flora and fauna. eDNA is a relatively cheap, fast and efficient method to non-destructively assess freshwater community composition and health. Ecological assessment will be applied to assess community health.
· Communication. Effective communication with supervisors and project partners is essential to manage to PhD work and deliver of the project objectives. Present information on research progress and outcomes both internally, to collaborators, to funders and at conferences. Publish research outcomes in appropriate journals and disseminate results of research through technical reports and industry press.
· Team work and interdisciplinary working. The integrated approach will combine different techniques, field work, lab work, bioinformatics and multiple project partners to look at river health. With the aim to develop a real-time digital river health assessment tool codesigned with the project partners. This will require integration of different datasets and holistic understanding of pollution, river health, method development and limitations. Work effectively with the other PhD students working on the Conwy Living Lab.
To apply visit our online applications portal: https://apps.bangor.ac.uk/apply/account/login/
Natural Environment Research Council funded RED ALERT Centre for Doctoral Training will provide training in water-based early warning systems for environmental and public health protection focused around 4 UK and 3 international Living Labs aimed to provide the in-depth knowledge and enable a step-change in managing environmental and public health.
